How to convert vcf format with 0/0 0/1 1/1 to SNP

Question

[taoyan]

Hello I have a vcf file like this:

#CHROM     POS     ID   REF ALT QUAL FILTER INFO    FORMAT  R4157   R4158   R4163
chr7    30902031    .    C   A   .      .    PR       GT     0/0     0/0     0/0

now I want to convert it to the format like that:

#CHROM    POS      ID   REF ALT QUAL    FILTER  INFO    FORMAT  R4157   R4158   R4163
chrC07  30902031    .    C   A   .         .     PR       GT     C        C       C

So could anyone know to to make it ?Thanks !!!

[WouterDeCoster]

What does C mean for an individual? Shouldn't that be CC for a diploid genome?

[taoyan]

yeah, C means CC, and if it is CA,we use N or Y to represent it

[Pierre Lindenbaum]

why do you want to do this ? what is your final aim ?

[taoyan]

Thank you for your reply!Now I get a GWAS result , and I want to analysis some genes if there are any snps located on them.Then I need to know whether these snps will affect the functions of genes!

[finswimmer]

Hello taoyan,

but than I think it is not a good idea to convert the genotypes in that way. A lot of programs work with the format 0/0 etc. as it is much faster to catch whether you have a reference or in alternative allele.

So please check first what the expected input for the programs you like to use is.

fin swimmer

Answer 1

[JC]

I'm assuming that you want to convert each VCF record into the genetic variant observed, so "0/0" is considered "C" and "1/1" is "A" and "0/1" is "CA".

#!/usr/bin/perl

use strict;
use warnings;

while (<>) {
  if (/^#/) {
    print;
    next;
  }
  chomp;
  my @a = split (/\t/, $_);
  my $ref = $a[3];
  my $alt = $a[4];
  for (my $i=9; $i <= $#a; $i++) {
    if ($a[$i] eq "0/0") {
      $a[$i] = $ref;
    } elsif ($a[$i] eq "1/1") {
      $a[$i] = $alt;
    } elsif ($a[$i] eq "0/1") {
      $a[$i] = "$ref$alt";
    } else {
      $a[$i] = "-";
    }
  }
  print join "\t", @a;
  print "\n";
}

this produces:

$ perl convertVariant.pl < file.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  R4157   R4158   R4163
chr7    30902031        .       C       A       .       .       PR      GT      C       C       C

[taoyan]

It works!!!Thank you!!!

[aman-coasab]

Hi, I am working on poplyploid crop and my VCF file have SNP data as 0/2, 1/2, 0/3, 2/3 etc in addition to standard 0/0, 1/1 and 0/1 SNP calling. Will this script work for my data? I tried to convert the VCF to hapmap using TASSEL which converted these codings to simple letters like R, S etc. depending upon SNPs, but its difficult to track down which allele has been marked to what letter. Thanks.

[JC]

Unfortunately it will not work for you, it is considering only a diploid genome (2 alleles), if you see 0/1/2/3 means it is tetraploid. Please post as a new question with an example of your VCF, I (and others) could modify the script to use that type of genomes.